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MolNFT v1 · #168791 · DNA

Self-assembly of a 3D DNA crystal lattice (4X5 duplex version) containing the J32 immobile holliday junction

6WR9 · DNA (5'- D(*GP*AP*GP*CP*AP*GP*AP*CP*TP*AP*GP*AP*CP*AP*CP*CP*…: “Self-assembly of a 3D DNA crystal lattice (4X5 duplex version) containing the J32 immobile holliday junction”. X-ray diffraction, 2 ligands (CAC, MG). MolNFT v1 #168791…

PDB
6WR9
Type
DNA
Length
42 nucleotides
Chains
4
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
DNA (5'- D(*GP*AP*GP*CP*AP*GP*AP*CP*TP*AP*GP*AP*CP*AP*CP*CP*AP*CP*TP*CP*A)- 3'); DNA…
Ligands
CAC, MG

Structure

x-ray diffraction · 4 distinct chains.

ChainMoleculeTypeResiduesSecondary structureUniProt
ADNA (5'- D(*GP*AP*GP*CP*AP*GP*AP*CP*TP*AP*GP*AP*CP*AP*CP*CP*AP*CP*TP*CP*A)- 3')dna21——
BDNA (5'-D(P*TP*GP*TP*CP*T)-3')dna5——
CDNA (5'-D(*TP*CP*TP*GP*AP*GP*TP*GP*G)-3')dna9——
DDNA (5'-D(P*AP*GP*TP*CP*TP*GP*C)-3')dna7——

Ligands and binding sites

  • CAC · Cacodylate ion · metal · 2 copies · chains B, C, D
  • MG · Magnesium ion · metal · chains B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Interfaces

5 interfaces between chains.

  • A–D · 346 Ų buried · 27 hydrogen bonds · nucleic-nucleic
  • A–C · 337 Ų buried · 24 hydrogen bonds · nucleic-nucleic
  • A–B · 227 Ų buried · 15 hydrogen bonds · nucleic-nucleic
  • B–C · 110 Ų buried · 3 hydrogen bonds · nucleic-nucleic
  • B–D · 88 Ų buried · 4 hydrogen bonds · nucleic-nucleic

Compared structures

  • 6WR9 · Self-assembly of a 3D DNA crystal lattice (4x5 duplex version) containing the J32… · the same entry in another collection · chain A against A, TM-score 1.00

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